Showing : ChIPseeker • reset
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ChIPseeker peak_Profile_Heatmap color palette
ChIPseeker
8 months ago Anton01 • 0
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283
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[ChIPseeker] Unable to perform gene ontology analysis
ChIPseeker
9 months ago Henry ▴ 10
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1
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564
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plotAvgProf - How to change labels in the facet option
ChIPseeker
updated 14 months ago by 67k • written 14 months ago by • 0
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2
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1.0k
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annotatePeak error for some problem
ChIPseeker
written 14 months ago by • 0
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1.5k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
23 months ago chavaleab • 0
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814
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Can ChiPseeker be as highly customizable as "computeMatrix"? for example if I want to plot the distribution of genes on the TAD boundary?
deeptools ChIPseeker
23 months ago 840842906 • 0
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1
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1.2k
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Create an Annotation DB file for a non-model organism
AnnotationDbi annotation ChIPseeker
updated 24 months ago by 67k • written 24 months ago by ▴ 50
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5.3k
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Cannot install packages in R/BiocManager_Warning message: package(s) not installed when version(s) same as or greater than current; use `force = TR…
Bioconductor BioCManager ChIPseeker
updated 2.1 years ago by 67k • written 2.1 years ago by • 0
1
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905
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Statistical test for genomic annotation by ChIPseeker
statistics PeakAnnotation ChIPseeker GuangchuangYu
2.5 years ago arisarkar88 ▴ 40
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1.1k
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Problem with "TxDb.Mmusculus.UCSC.mm39.refGene" to annotate genes with ChIPseeker
TxDb.Mmusculus.UCSC.mm39.refGene ChIPseeker annotate
2.6 years ago Palmira • 0
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2.9k
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How to define 'distal intergenic'
ChIPseeker
2.7 years ago Sanghoon • 0
0
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1
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1.3k
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ChIP-seq peak annotation to gene in ChIPseeker
ChIPseeker
2.7 years ago Gyan Prakash Mishra ▴ 10
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901
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Can we get an Average Profile of ChIP peaks binding to Transcription "START and STOP site" both in a single plot?
ChIPSeq ChIPseeker
2.8 years ago Swadha • 0
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952
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What is weightcol doing in getTagMatrix() function of ChIPseeker?
ChIPseeker
2.9 years ago hyjforesight • 0
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1
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2.1k
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ChIPseeker issue with plotpeakProf2 when making plot of peak profile across gene body and flanks
ChIPseeker
3.3 years ago william.ho • 0
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2
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1.3k
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getPromoters
ChIPseeker
3.3 years ago guoyou88 • 0
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968
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ChIPseeker, how to customize plotDistToTSS
ChIPseeker
3.3 years ago alexandre.blais ▴ 50
1
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3
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1.2k
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what does " * " denote under the strand column of the GRanges object file output
ChIPseeker
3.6 years ago Meghna • 0
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0
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1.1k
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CHIPseeker- promoter gene names
ChIPseeker CHIPsee
3.7 years ago rb • 0
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1
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1.8k
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ChIPseeker: Annotating Peaks with both upstream and downstream gene
ChIPseeker
updated 3.8 years ago by ▴ 10 • written 3.8 years ago by ▴ 10
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1.0k
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What is the definition of flank_gene_distances output field in ChIPseeker
ChIPseeker
3.8 years ago Sam ▴ 10
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1.3k
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Annotation of downstream in ChIPseeker
downstream Priority ChIPseeker
3.8 years ago Xiaojie Cheng • 0
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2
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1.3k
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ChIPseeker failing on r-devel on CRAN checks
ChIPseeker cinaR
3.9 years ago Onur Karakaslar • 0
1
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4
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2.7k
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Genome annotation file in TxDb.Mmusculus.UCSC.mm10.knownGene
ChIPseeker TxDb.Mmusculus.UCSC.mm10.knownGene
4.0 years ago • updated 3.9 years ago Kasit • 0
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916
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ChIPSeeker covplot function, fix yaxis
ChIPseeker
4.0 years ago jordi.planells • 0
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0
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920
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Genes in ChIPseeker annotation do not exist in the organism
ChIPseeker
4.2 years ago Sam ▴ 10
2
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2
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2.8k
views
ChIP seeker annotation error
DiffBind chipseq ChIPseeker ChipDb annotation
4.2 years ago • updated 4.0 years ago Mar Mar ▴ 20
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3
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2.2k
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importing BED with non-integer values
ChIPseeker ChIPSeqData
updated 4.2 years ago by 67k • written 4.2 years ago by ▴ 10
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0
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774
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Regarding hiding or removing the vertical line at center (at zero coordinate) average profile in Chipseeker
ChIPseeker
4.2 years ago Prasoon • 0
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1
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1.9k
views
How to use peak summits instead of TSS or transcript to plot heatmap for other factors
ChIPseqR ChIPs ChIPseeker ChIPSeq chipseq
updated 4.3 years ago by 67k • written 4.3 years ago by • 0
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1.1k
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About metadata columns in Grange objects required for ChIPseeker analysis
ChIPseeker
4.3 years ago ahua217 ▴ 10
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937
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How to get the raw numbers of annotated features by ChIPseeker?
ChIPseeker
4.3 years ago bioinfouser2 ▴ 10
2
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1
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2.4k
views
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
ChiPseeker plotAnnoPie
4.4 years ago amafon95 ▴ 20
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1
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1.1k
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p value after enrichPeakOverlap analysis in ChIPseeker
ChIPseeker
updated 18 months ago by • 0 • written 4.5 years ago by • 0
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0
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1.1k
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ChIPseeker error when I wnat to get tagMatrix
Chipseeker TxDb getpromoters software error
4.7 years ago hfyuan2016 • 0
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0
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984
views
Potential oversimplification in the overlap function
ChIPseeker
4.7 years ago konsta.kukkonen • 0
1
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0
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1.1k
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Functional enrichment analysis issue/ChIPseeker package
ChIPseeker
4.7 years ago egbastakis • 0
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1
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2.0k
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ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
4.8 years ago Assa Yeroslaviz ★ 1.5k
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1
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1.2k
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ChIPSeeker - options(ChIPseeker.downstreamDistance = 500) seems not work
ChIPseeker
5.0 years ago Guandong Shang ▴ 40
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1
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1.9k
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Using EnsDb.Hsapiens.v86 database doesn't fetch the ENSEMBL IDs
ChIPseeker
5.4 years ago sutturka • 0
1
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2
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4.1k
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Unable to annotate the differential peaks from DiffBind using ChIPseeker
chip seq ChIPseeker peak annotation annotatePeak() Diffbind
5.4 years ago researcher • 0
2
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1
reply
4.4k
views
Finding the proper universe for enrichGO and enrichKEGG - only the genes that are annotated in those ontologies
chipseeker ChIPseeker
5.5 years ago endrebak85 ▴ 40
1
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3
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1.4k
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Error: package or namespace load failed for 'ChIPseeker': 'TxDb.Hsapiens.UCSC.hg19.knownGene' is not exported from 'namespace: TxDb.Hsapiens.UCSC.hg1…
chipseq chipseeker R Bioconductor
updated 5.6 years ago by 25k • written 5.6 years ago by ▴ 10
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1
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3.1k
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error in readPeakFile {chipseeker}
ChIPseeker readPeakFile
5.7 years ago Theo ▴ 10
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1
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1.4k
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Problem in using covplot ChIPseeker
ChIPseeker software error
5.9 years ago vasudha.sharma • 0
3
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2
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2.1k
views
How to use EnsDb in annotatePeak from package "ChIPseeker"
GRanges ChIPseeker annotatePeak TxDb EnsDb
updated 6.0 years ago by ★ 2.1k • written 6.0 years ago by ▴ 100
1
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1
reply
2.0k
views
ChIPseeker genomicAnnotationPriority
annotation chipseeker
updated 3.5 years ago by • 0 • written 6.1 years ago by ▴ 10
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0
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1.3k
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How to use ChIPseeker for getting genebody annotations.
chipseeker chipseq
6.1 years ago bioinfouser2 ▴ 10
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2
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1.4k
views
how to get frequencies from plotDistToTSS
chipseeker
6.1 years ago KKO • 0
1
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0
replies
1.3k
views
ChipSeeker Flanking gene annotation
chipseeker
6.3 years ago Lauma R ▴ 10
50 results • Page 1 of 1
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Comment: displaying the differential expression with deseq2 over 4X2 samples with the in by Martijn • 0
thanks James, but if I do pairwise analyses per subject, I get the impression that I only get the intercepts per gene. Do you mean regardin…
Comment: plyranges: find exact GRanges match keeping metadata columns by alexis.weinreb • 0
Thank you, this does clarify the available options.
Answer: displaying the differential expression with deseq2 over 4X2 samples with the in by James W. MacDonald 67k
If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated a…
Answer: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by jodan • 0
Your approach sounds solid! You might also consider plotting a scatter plot comparing log2 fold changes from both datasets to identify gene…
Answer: Unused arguments error without used arguments in GSVA? by jodan • 0
It looks like the ssgseaParam function might not be passing the correct parameters to GSVA::gsva(). The error suggests that minSize and max…
Votes
Answer: Find exact GRanges match keeping metadata columns
Answer: Find exact GRanges match keeping metadata columns
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
Answer: Unused arguments error without used arguments in GSVA?
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